Contacts of the strand formed by residues 36 - 42 (chain A) in PDB entry 2VSC
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 36 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A MET* 4.1 9.6 - - + -
30A ALA* 3.7 25.4 - - + -
32A ASN 4.0 7.2 - - - +
33A THR* 2.9 8.3 + - - +
34A THR 3.4 0.4 - - - +
35A GLU* 1.3 83.1 - - - +
37A TYR* 1.3 68.6 + - - +
38A VAL* 4.2 1.3 - - + -
50A PHE* 4.2 2.1 - - - +
52A GLY* 3.0 27.4 + - - -
53A ALA 4.4 1.0 + - - -
73A LEU* 3.6 37.9 - - + -
74A LEU* 4.0 14.4 - - + -
98A VAL* 4.1 10.5 - - + -
99A THR 3.2 9.2 - - - +
100A GLU* 4.6 1.8 - - + -
101A LEU* 5.2 3.1 - - - +
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Residues in contact with TYR 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A VAL* 1.3 73.0 - - - +
38A VAL* 1.3 89.4 + - - +
39A LYS* 4.2 21.8 - - + -
49A THR* 3.8 23.4 + - - +
50A PHE 3.5 9.4 - - - -
51A ASP* 3.6 38.5 - - + +
97A GLU* 3.9 5.2 - - - +
98A VAL* 3.4 4.9 - - - +
99A THR* 2.8 47.9 + - - +
101A LEU* 4.6 14.8 - - + -
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Residues in contact with VAL 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A VAL* 4.2 1.6 - - + -
37A TYR* 1.3 81.3 - - - +
39A LYS* 1.3 63.2 + - - +
40A TRP* 3.8 29.4 - - + +
48A TYR* 4.7 3.4 - - + -
49A THR* 3.0 6.8 - - - -
50A PHE* 2.7 40.4 + - + +
68A ILE* 4.0 22.2 - - + -
73A LEU* 3.7 36.3 - - + -
78A ALA* 4.2 15.5 - - + -
96A CYS* 5.0 0.9 - - - -
97A GLU 3.3 7.2 - - - +
98A VAL* 4.5 5.2 - - + -
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Residues in contact with LYS 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A TYR* 4.2 18.8 - - + -
38A VAL* 1.3 74.9 - - - +
40A TRP* 1.3 64.3 + - - +
41A LYS* 3.6 28.0 - - + +
46A ASP* 3.4 41.3 + - + +
48A TYR 3.3 3.1 - - - +
49A THR* 3.9 12.3 - - + -
95A THR 3.6 1.6 - - - +
96A CYS* 3.7 0.3 - - - -
97A GLU* 2.8 65.0 + - + +
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Residues in contact with TRP 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ILE* 3.4 41.7 - - + -
22A PRO 3.8 2.9 - - - -
23A CYS* 3.5 17.9 - - + -
38A VAL* 3.8 21.5 - - + +
39A LYS* 1.3 72.7 - - - +
41A LYS* 1.3 55.8 + - - +
46A ASP* 3.5 3.5 - - - -
47A ILE* 2.7 49.2 + - + +
48A TYR* 2.7 21.3 + + + +
68A ILE* 4.0 2.6 - - + +
78A ALA 2.9 29.2 + - - -
80A LEU* 3.5 37.4 - - + +
94A TYR* 3.9 24.2 - + + -
95A THR 3.2 16.2 - - - -
96A CYS* 3.6 21.3 - - + -
109B ILE* 3.9 4.7 - - + -
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Residues in contact with LYS 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A LYS* 3.6 29.0 - - + +
40A TRP* 1.3 78.9 - - - +
42A PHE* 1.3 61.2 - - - +
44A GLY* 5.4 6.3 - - - +
45A ARG 3.2 13.0 - - - +
46A ASP* 3.7 17.8 + - - +
47A ILE* 4.3 1.3 - - - -
93A ASN 4.1 0.6 - - - +
94A TYR* 3.3 9.0 - - - +
95A THR* 2.8 52.5 + - + +
97A GLU* 3.8 27.7 + - - -
106B GLU* 5.5 4.0 + - - -
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Residues in contact with PHE 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LYS* 1.3 74.7 - - - +
43A LYS* 1.3 104.2 + - + +
44A GLY 3.3 0.4 - - - -
45A ARG* 3.0 28.1 + - - +
47A ILE* 3.9 19.7 - - + +
63A PHE* 4.0 14.1 - + + -
89A SER 5.3 0.4 - - - -
90A HIS* 3.6 39.3 - + + -
91A THR 3.3 30.7 - - - -
92A GLY* 4.0 7.4 - - - -
93A ASN 3.7 14.4 - - - -
94A TYR* 3.6 24.9 - + + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il